Thousands of civilians are seeking shelter at UN bases in South Sudan after a second night of fighting between factions of the national army. A UN official said 13,000 people had sought refuge in the capital, Juba.

A number of high-profile government critics, including at least seven former ministers, have been arrested. "The way they're going after people is really causing fear," said Susan Page, the US ambassador.

Juba's military hospital has received around 400 casualties amid reports of fighting in multiple locations across the city. "We've lost a lot of people," said one of the doctors. At least 20 more were being treated at the Juba teaching hospital, where Dr Wani Mena said most of the patients were suffering from gunshot wounds.

South Sudan's foreign minister said on Tuesday that the military had "cleared out remnants" of a faction accused of mounting a coup attempt. "They are still looking for more … who are suspected of being behind the coup," Barnaba Marial Benjamin said.

The former vice-president, Riek Machar, who is accused of orchestrating the alleged coup attempt, is believed to be in hiding.

The hunt for Machar, an influential politician and one of the heroes of the brutal war of independence waged against Sudan, threatens to cause further political upheaval in the world's youngest country, where the president, Salva Kiir, has been locked in a power struggle with his former deputy for months.

Kiir fired Machar, who is also deputy leader of the ruling Sudan People's Liberation Movement, as vice-president in July. Machar has said he will contest the presidency in 2015, and has openly criticised Kiir, saying that if the country is to be united it cannot tolerate a "one man's rule" or "dictatorship".

Kiir sacked his entire cabinet along with Machar, prompting the US and EU to call for calm amid fears the move could destabilise the country.

The office of the UN secretary general, Ban Ki-moon, said in a statement that he was "deeply concerned about reports of fighting" and "about the risk of targeted violence against certain communities". He urged the country's military leaders to "impose discipline on their forces and to exercise maximum restraint in the use of force".

The oil-rich east African nation has been plagued by ethnic tension since it broke away from Sudan in 2011. In the rural state of Jonglei, where the government is trying to put down a rebellion by a former colonel in the country's armed forces, the military faces charges of widespread abuses against the Murle ethnic group of the rebels' leader, David Yau Yau.

Thousands of people have been displaced from their homes, many seeking refuge across the border in Sudan.